My situation is the following: This user is the admin of a site which has 5GB allocated, when I created his user account I gave him 50 MB thinking if he needs more he can allocate it himself.
My question now is this: he is using the shell access (I guess using sftp) to transfer his huge website (lots of photos) to my server, but when he is copying files they will belong to the following owner: web19_tibi:web19 (which is normal) but does this mean I will always get warnings that he exceeded his quota? Do you have to set the quota of the administrator equal to the quota of the site itself?
How does quota work?

but does this mean I will always get warnings that he exceeded his quota?

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Yes.

Tenaka said:

Do you have to set the quota of the administrator equal to the quota of the site itself?

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Not necessarily, but you have to keep in mind that it's the admin who uploads all the files to the web folder so he should get a reasonable quota. If your web site has a quote of 5 GB, then I'd give the admin at least 500 MB.

If a web site has only the admin user, then it sure makes sense to give the admin the same quota than the web site. But if you have more than one user, you should also give the other users some web space which decreases the space you can give to the admin.

would that allocate 10 MB to the user and 50MB-x= to the admin? x meaning whatever the user does not use, so if the admin imediately takes up 45MB the user would only have 5 MB ?

Of course these users would be the only ones on this site.

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The admin user would have unlimited space, but he belongs to the web group, and that group has only 50 MB. So if the admin user uses FTP to upload files, the files will belong to him and the web group, and therefore he cannot exceed the web group quota. If user1 has used 10 MB so far, that would be 40 MB.

If the admin user (in our example) with no quota uses 50 MB, then there's no more space left for user1 with 10 MB because both users belong to the same group, and the group has a quota of 50 MB.
So it is a good idea to give everyone a reasonable quota.